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- PDB-9lpc: Crystal structure of Escherichia coli trptophanyl-tRNA synthetase... -

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Basic information

Entry
Database: PDB / ID: 9lpc
TitleCrystal structure of Escherichia coli trptophanyl-tRNA synthetase in complex with tRNA(Trp)
Components
  • Tryptophan--tRNA ligase
  • tRNA(Trp)
KeywordsLIGASE/RNA / trptophanyl-tRNA synthetase / tRNA / complex / LIGASE-RNA complex
Function / homology
Function and homology information


tryptophan-tRNA ligase / tryptophanyl-tRNA aminoacylation / tryptophan-tRNA ligase activity / ATP binding / cytosol
Similarity search - Function
Tryptophan-tRNA ligase, bacterial-type / : / Tryptophan-tRNA ligase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
: / RNA / RNA (> 10) / Tryptophan--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsPeng, X. / Chen, B. / Zhou, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22177140 China
CitationJournal: To Be Published
Title: The lineage-specific tRNA recognition mechanism of bacterial trptophanyl-tRNA synthetase and its implications for inhibitor discover
Authors: Peng, X. / Xia, K. / Huang, Q. / Xiang, M. / Han, L. / Qiu, H. / Gu, Q. / Chen, B. / Zhou, H.
History
DepositionJan 24, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 7, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tryptophan--tRNA ligase
B: Tryptophan--tRNA ligase
C: tRNA(Trp)
D: tRNA(Trp)


Theoretical massNumber of molelcules
Total (without water)125,0144
Polymers125,0144
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7670 Å2
ΔGint-64 kcal/mol
Surface area47080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.788, 63.206, 91.629
Angle α, β, γ (deg.)98.50, 97.25, 100.04
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Tryptophan--tRNA ligase / Tryptophanyl-tRNA synthetase / TrpRS


Mass: 38373.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: trpS, ACU57_16550, B6R15_000448, B6R31_002275, BANRA_02015, BCB93_002501, BGM66_002290, BGZ_04191, BK383_21195, BKL28_001915, BMT91_03555, BvCmsNSP007_00090, BXT93_04920, C0P57_000786, C2R31_ ...Gene: trpS, ACU57_16550, B6R15_000448, B6R31_002275, BANRA_02015, BCB93_002501, BGM66_002290, BGZ_04191, BK383_21195, BKL28_001915, BMT91_03555, BvCmsNSP007_00090, BXT93_04920, C0P57_000786, C2R31_002885, C3F40_19370, CG704_07870, CIG67_21025, CTR35_001866, D9D43_04205, DD762_12005, DL968_00250, DNQ45_04190, DTL43_13995, DU321_12325, E4K51_10330, E6D34_04225, EIA08_11870, EPS97_04620, F7F11_12075, F7N46_14665, F9413_17445, F9461_03030, F9B07_12605, FGAF848_25410, FKO60_13960, FOI11_018845, FOI11_04335, FPS11_03390, FZU14_04195, G3V95_06005, G4A38_16925, G4A47_18515, G5603_11025, GAI89_06310, GNW61_08470, GOP25_12480, GP944_08250, GQE86_01825, GQN24_10725, HEP34_002452, HI055_002233, HJQ60_002846, HL563_11055, HL601_09110, HLX92_09755, HLZ50_06610, HMV95_07850, HVW04_17215, HVW43_18350, HVY77_01760, I6H00_19775, IH772_08800, J0541_002134, JNP96_25720, NCTC10764_03793, NCTC10974_00460, NCTC9044_01447, NCTC9073_00479, NCTC9077_00527, NCTC9706_02656, P6223_000209, Q2V20_09290, QDW62_01780, QO046_14075, R8G00_13645, SAMEA3472044_01080, SAMEA3472056_01981, SAMEA3752557_02035
Production host: Escherichia coli (E. coli) / References: UniProt: E2QFN4, tryptophan-tRNA ligase
#2: RNA chain tRNA(Trp)


Mass: 24133.295 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) / References: GenBank: 1841774800
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.59 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.5 M ammonium acetate, 0.1 M HEPES pH 7.5, 16% w/v PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97954 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97954 Å / Relative weight: 1
ReflectionResolution: 2.82→89.51 Å / Num. obs: 30805 / % possible obs: 97.4 % / Redundancy: 3.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.027 / Rrim(I) all: 0.05 / Net I/σ(I): 21.2
Reflection shellResolution: 2.82→2.87 Å / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1346 / CC1/2: 0.795 / Rpim(I) all: 0.356 / Rrim(I) all: 0.61

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
DIALSdata scaling
xia2data reduction
MERLOTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8I1Y

8i1y


Resolution: 2.82→59.12 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 31.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2711 1472 4.79 %RANDOM
Rwork0.2364 ---
obs0.238 30742 97.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.82→59.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4577 2879 0 7 7463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017872
X-RAY DIFFRACTIONf_angle_d1.20711369
X-RAY DIFFRACTIONf_dihedral_angle_d18.4853151
X-RAY DIFFRACTIONf_chiral_restr0.0691418
X-RAY DIFFRACTIONf_plane_restr0.008979
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.82-2.910.35871200.37912387X-RAY DIFFRACTION87
2.91-3.020.36821490.33072638X-RAY DIFFRACTION97
3.02-3.140.35271430.31722667X-RAY DIFFRACTION98
3.14-3.280.29431430.2962669X-RAY DIFFRACTION97
3.28-3.450.32071320.28342686X-RAY DIFFRACTION98
3.45-3.670.30211410.25892698X-RAY DIFFRACTION99
3.67-3.950.28051180.23312743X-RAY DIFFRACTION98
3.95-4.350.25071480.21922665X-RAY DIFFRACTION99
4.35-4.980.24981430.20552680X-RAY DIFFRACTION98
4.98-6.270.26341190.22992737X-RAY DIFFRACTION99
6.27-59.120.22131160.19652700X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.29980.1911-0.09771.9573-0.13010.5424-0.09570.02130.69660.19970.1345-0.46270.41090.0475-0.12030.9783-0.1260.00890.78610.0241.30528.625534.340313.5075
29.0999-3.75280.99419.3319-4.51285.91180.7032-0.3631-0.2045-0.90610.0668-0.01780.9870.3427-0.63820.85970.03120.10591.12850.30641.18422.725450.06389.8541
31.5911-0.0486-0.65630.4428-0.11031.54590.66270.74650.1082-0.6279-0.46281.3758-0.9664-0.6964-0.25521.17010.22690.14811.22750.11921.758322.952327.3044-4.5403
42.63231.6975-0.69721.718-0.01692.89450.42060.71731.1575-0.43680.0844-0.3391-0.82920.0837-0.67660.842-0.05930.08790.81130.12520.844328.571618.499-13.0287
53.9270.73912.43084.5627-0.41891.46350.0522-0.1061-0.2505-0.0954-0.1281-0.58950.11580.20730.12580.791-0.02340.03070.61410.07131.04894.972343.573211.3604
62.5453-0.14060.84533.4184-1.04041.9827-0.1917-0.5066-0.25960.4820.158-0.0088-0.3529-0.6388-0.00610.95950.077-0.060.93860.22730.8986.1252-0.230437.5363
72.1878-1.69741.431.9214-0.46790.9542-1.163-1.74790.41021.2340.53640.1914-1.1729-1.09410.54461.55010.4827-0.06531.9005-0.12421.02492.15454.305256.9306
81.37550.4774-0.45850.1706-0.14920.1091-0.5194-0.9578-0.5114-0.5871-0.60410.0614-0.1560.24880.86732.71990.25250.37223.0587-0.7661.2623-22.678517.18766.4438
96.47097.12387.11158.10997.67437.97990.1073-2.64170.96641.465-1.16631.36031.471-2.04521.02311.68360.4530.13711.8016-0.080.9522-1.5552-4.003253.4958
102.47210.02231.70821.96670.05325.1867-0.0015-0.6999-0.29020.68150.52470.51790.63960.1656-0.62931.24310.29240.04431.14960.20770.830410.8784-14.89250.4725
112.6130.52821.50663.9115-0.69541.4777-0.20430.1729-0.04430.08550.4656-0.00810.23540.7792-0.14010.68030.0750.05030.81350.06910.6268.5785-3.022534.3943
121.8592-1.1678-0.33811.13070.05882.8481-0.01550.38950.043-0.0689-0.052-0.08520.02410.24770.04530.3852-0.0616-0.01860.52310.0540.464-6.18433.53815.9283
132.7161-0.1206-2.16870.06010.09232.82570.07360.0264-0.3055-0.1707-0.11550.05650.0410.36570.01580.60290.0285-0.00750.6550.01360.57714.24920.67284.0663
142.48610.0378-1.02741.28540.28170.99270.02991.3066-0.6365-0.25260.01530.00650.17610.05330.01560.81270.0202-0.03461.0449-0.13230.690714.9799-2.4385-15.7336
152.53370.6942-0.54880.31670.08460.2922-0.04330.6644-0.05310.03550.07960.27030.4022-1.159-0.04190.6202-0.044-0.00950.7655-0.04540.8367-23.3278-0.6929.2561
162.60070.2959-0.21572.6779-1.35761.7014-0.0697-0.54520.24650.53350.16830.5034-0.4664-0.1821-0.07410.610.04460.02790.5364-0.09410.5919-28.117615.449226.9723
171.8587-1.90631.60263.7639-2.24594.3393-0.2335-1.0858-0.54331.49580.2718-0.7043-0.7665-0.0301-0.04570.92630.0359-0.13610.77960.07520.7764-4.393318.613228.4159
182.53-0.80440.5711.7148-1.0050.7227-0.0182-0.35850.77180.21270.06730.177-0.2546-0.02240.0290.6576-0.0328-0.02670.5281-0.05110.8209-16.808923.715120.6137
192.8697-1.0599-2.55042.33323.06894.1865-0.1085-0.41190.88720.13510.19760.1263-0.27990.00350.45880.75480.05920.0040.741-0.02991.0802-23.172929.584923.7655
201.40050.50630.02440.7440.06940.0393-0.4543-0.69050.75810.4953-0.4166-0.1999-0.3598-0.02370.50921.69390.89660.0771.1143-1.01450.3016-22.108619.302548.5247
211.3454-0.41651.0292.359-0.10420.8905-0.2714-0.65330.40390.87520.26190.4768-0.0692-0.45840.05270.830.09810.0740.926-0.15220.8315-33.453117.897937.0701
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 1 through 15 )
2X-RAY DIFFRACTION2chain 'C' and (resid 16 through 20 )
3X-RAY DIFFRACTION3chain 'C' and (resid 21 through 30 )
4X-RAY DIFFRACTION4chain 'C' and (resid 31 through 45 )
5X-RAY DIFFRACTION5chain 'C' and (resid 46 through 73 )
6X-RAY DIFFRACTION6chain 'D' and (resid 1 through 10 )
7X-RAY DIFFRACTION7chain 'D' and (resid 11 through 27 )
8X-RAY DIFFRACTION8chain 'D' and (resid 28 through 38 )
9X-RAY DIFFRACTION9chain 'D' and (resid 45 through 49 )
10X-RAY DIFFRACTION10chain 'D' and (resid 50 through 59 )
11X-RAY DIFFRACTION11chain 'D' and (resid 60 through 73 )
12X-RAY DIFFRACTION12chain 'A' and (resid 3 through 150 )
13X-RAY DIFFRACTION13chain 'A' and (resid 151 through 221 )
14X-RAY DIFFRACTION14chain 'A' and (resid 222 through 298 )
15X-RAY DIFFRACTION15chain 'A' and (resid 299 through 340 )
16X-RAY DIFFRACTION16chain 'B' and (resid 3 through 98 )
17X-RAY DIFFRACTION17chain 'B' and (resid 99 through 122 )
18X-RAY DIFFRACTION18chain 'B' and (resid 123 through 168 )
19X-RAY DIFFRACTION19chain 'B' and (resid 169 through 188 )
20X-RAY DIFFRACTION20chain 'B' and (resid 189 through 206 )
21X-RAY DIFFRACTION21chain 'B' and (resid 207 through 334 )

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